GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Escherichia coli BW25113

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Keio:17511
          Length = 356

 Score =  305 bits (781), Expect = 1e-87
 Identities = 170/352 (48%), Positives = 226/352 (64%), Gaps = 25/352 (7%)

Query: 17  VGSLQLKTIRKAF-GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGS 75
           +  L+L+ + K++ G  +V+K + LDV DGEF++ VGPSGCGKSTLLR +AGLE  T G 
Sbjct: 1   MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60

Query: 76  VQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAG 135
           + I+   V  + P  RGIAMVFQ+YALYPH++V++NM  GLK  G+ K +I E+V +AA 
Sbjct: 61  IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR 120

Query: 136 MLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARL 195
           +L L+  L RRP ELSGGQRQRVA+GRAIVR+P +FLFDEPLSNLDA LRV  RLE+ +L
Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL 180

Query: 196 HRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQM 255
           HR LK T +YVTHDQVEAMTLA +++V+N G  EQ+G+P+E+Y +PA+LFVA FIGSP M
Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM 240

Query: 256 NFIEAAKLGD----------------------GEAKTIGIRPEHIGLSRESGDWKGKVIH 293
           N +      +                      G   T+GIRPEHI LS ++      V+ 
Sbjct: 241 NLLTGRVNNEGTHFELDGGIELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEGGVPMVMD 300

Query: 294 -VEHLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDAD 344
            +E LGAD + +       L+ VRL  + R      +        +H FD +
Sbjct: 301 TLEILGADNLAHGRWGEQKLV-VRLAHQERPTAGSTLWLHLAENQLHLFDGE 351


Lambda     K      H
   0.320    0.137    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 340
Number of extensions: 13
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 352
Length of database: 356
Length adjustment: 29
Effective length of query: 323
Effective length of database: 327
Effective search space:   105621
Effective search space used:   105621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory